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Do you have the option to generate lightmap UVs enabled on your mesh settings? If not, it uses regular UVs which can overlap, causing issues like the one seen above.

If you are generating lightmap UVs, then the only other thing I can think of would be overlapping surfaces. If there are two triangles in basically the same place, the lightmapper may get confused as to which is shadowing which, and that could also cause issues.